Pigmentation biosynthesis influences the microbiome in sea urchins

Abstract

Organisms living on the seafloor are subject to encrustations by a wide variety of animals, plants and microbes. Sea urchins, however, thwart this covering. Despite having a sophisticated immune system, there is no clear molecular mechanism that allows sea urchins to remain free of epibiotic microorganisms. Here, we test the hypothesis that pigmentation biosynthesis in sea urchin spines influences their interactions with microbes in vivo using CRISPR/Cas9. We report three primary findings. First, the microbiome of sea urchin spines is species-specific and much of this community is lost in captivity. Second, different colour morphs associate with bacterial communities that are similar in taxonomic composition, diversity and evenness. Lastly, loss of the pigmentation biosynthesis genes polyketide synthase and flavin-dependent monooxygenase induces a shift in which bacterial taxa colonize sea urchin spines. Therefore, our results are consistent with the hypothesis that host pigmentation biosynthesis can, but may not always, influence the microbiome in sea urchin spines.

Keywords: echinoderm; flavin-dependent monooxygenase; host–microbe symbiosis; microbial communities; polyketide pigments; polyketide synthase.

Figure 1.

Specificity in the spine microbiome between sea urchin species. (a) Community similarity of the spine bacterial communities of seven sea urchin species, as estimated by unweighted UniFrac for membership (left) and weighted UniFrac for composition (right). (b) The corresponding diversity estimates via phylogenetic diversity (left) and dominance (right) as well as (c) phylum-level profiles of the bacterial communities. (Online version in colour.)

Figure 2.

Colour morphs and their pigmentation chemistry. Aboral photographs (left) and high-performance liquid chromatography profiles of spine pigments from green (first row), red (second row) and white (third row) colour morphs of Lytechinus variegatus, as well as from Strongylocentrotus purpuratus (fourth row) (Sp, spinochrome; Ech, echinochromes). (Online version in colour.)

Figure 3.

Consistency in the spine microbiome between colour morphs of Lytechinus variegatus. (a) Similarity in the membership (unweighted UniFrac) and composition (weighted UniFrac) of the bacterial communities associated with the spines of each colour morph. (b) Estimates of α diversity for each colour morph, as measured by Faith's phylogenetic diversity (left) and McIntosh dominance (right). (c) Genus-level profiles of these bacterial communities. (d) ASV similarity between the green, red and white colour morphs. (Online version in colour.)

Figure 4.

Pigmentation phenotypes. Phenotypes of (a) the wild-type, (b) polyketide synthase knockout (PKS) and (c) flavin-dependent monooxygenase knockout (Fmo3) in the sea urchin Hemicentrotus pulcherrimus that were established by CRISPR/Cas9 mutagenesis. (Online version in colour.)

Figure 5.

Pigment composition influences the spine microbiome. (a) Community similarity of the spine bacterial communities of wild-type, PKS knockout and Fmo3 knockout in the sea urchin Hemicentrotus pulcherrimus, as estimated by unweighted UniFrac for membership (left) and weighted UniFrac for composition (right). (b) The corresponding diversity estimates via phylogenetic diversity (left) and dominance (right), as well as (c) phylum-level profiles of the bacterial communities and (d) ASV similarity between treatments. (Online version in colour.)